Hidden Grotto - RNGing for encounters using RNG Reporter 9.96.5 beta
The encounter slots for Hidden Grottoes are in the 5th Gen Tools drop-down menu. This guide will use the first two tabs on the encounter slot page, which are titled D-Black2 and D-White2. The percentage value listed next to each individual Pokémon is the percent the encounter can be female. Note that this doesn't match the actual gender ratio. There are 11 slots (listed vertically) and 4 sub-slots (listed horizontally).
Every 256th step the player takes is when every unoccupied Grotto will run a check to generate, and they generate in the order listed on the encounter slot page. The order is VERY important. Unlike the 128-step counter, this step counter is not saved. If you've played through the entire game without ever visiting a Grotto it's a safe bet to assume they're all filled. EVERY Hidden Grotto listed before the one you want to RNG the encounter in MUST be occupied by either an item (hidden or not) or a Pokémon. This is EXTREMELY important. Also, make sure the Day Care is holding no Pokémon. Walking with Pokémon in the Day Care will advance the PIDRNG past your target.
You'll want to save in the Grotto that you wish to RNG the encounter for. Have any Pokémon you may need (capture, sync, etc.). If it's occupied then take the item (which may or may not be hidden) or faint/capture the Pokémon prior to saving.
The example this guide will use is RNGing a female Vulpix from the Grotto in Abundant Shrine (labeled as Abundant [Field] in the encounter slot page). First, a picture and then the explanation on how to use the searcher:

Slot - The 11 slots that are listed vertically. Vulpix is 0 so check it.
SubSlot - The 4 horizontal slots. Vulpix is in all of them so check all of the boxes 0 to 3.
Gender - We want female so choose F. If you don't care you can leave it blank and it will display both M and F seeds. Leave blank for genderless Pokémon.
Gender Ratio - The percentage listed on the encounter table. NOT the actual ratio. Make sure you select the right one for it to filter through the proper gender in the search results. Leave blank for genderless. For Vulpix it's 10% so choose 10.
With that all filled out let's run the search:

You'll notice that you'll get a lot of results FAST. This is normal. Now pick one that you like (this example picks the highlighted one), copy the seed, and paste it into the main window with the proper settings like so:

While it probably isn't necessary to fill out the relevant encounter info (Hidden Grotto encounter type and gender ratio for the actual ratio of the Pokémon) this WILL be required when you actually RNG the Pokémon. Anyways, the purpose of doing this is to find out the starting PIDRNG frame of this seed. In this case it's 54, which matches the frame on the Time Finder. This means you do not have to do any PIDRNG advancements. Simply walk the 256 steps, leave, and re-enter the Grotto. If you have to do any advancements you need to do them before walking the 256 steps. There is no need to verify your seed via Chatot pitches for this as you will immediately know whether you hit your seed or not.
For RNGing the actual encounter it's almost the same as a stationary encounter, except use Hidden Grotto as the encounter type and it cannot be shiny. You MUST use the correct settings on the Time Finder and the main window or else you WILL get the wrong nature. This includes the actual gender ratio with the gender the encounter is set to. In this example you would use Female (25% Male/75% Female).